chroGPS
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see chroGPS.
chroGPS2: Generation, visualization and differential analysis of epigenome maps
Bioconductor version: 3.11
We provide intuitive maps to visualize, analyze and compare the association between genetic elements based on their epigenetic profiles. The approach is based on Multi-Dimensional Scaling, and includes a parallelized implementation for handling high dimensional datasets. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds. We also provide functions and methods to perform differential analysis of epigenome maps at factor and gene level.
Author: Oscar Reina, David Rossell
Maintainer: Oscar Reina <oscar.reina at irbbarcelona.org>
citation("chroGPS")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("chroGPS")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ChIPSeq, ChIPchip, Clustering, DataRepresentation, Epigenetics, HistoneModification, ImmunoOncology, Software, Visualization |
| Version | 2.6.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
| License | GPL (>=2.14) |
| Depends | R (>= 3.2.0), GenomicRanges, IRanges, methods, Biobase, MASS, graphics, stats, changepoint |
| Imports | cluster, DPpackage, ICSNP, ellipse, vegan |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | parallel, XML, rgl, gplots, pheatmap, ChIPpeakAnno, org.Dm.eg.db, caTools, plotly |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/chroGPS |
| Source Repository (Developer Access) | git clone [email protected]:packages/chroGPS |
| Package Short Url | https://bioconductor.org/packages/chroGPS/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |